Freesurfer

freesurfer@nmr.mgh.harvard.edu

11 participants
30080 discussions

Re: [Freesurfer] qdec error: ERROR reading lh.cortex.label
by Wen, Wei 05 May '08

05 May '08

- Thanks Doug. Do I need to rerun everything or at least rerun the average step? I went straight into qdec but the same error message appears (after replacing the old mri-mergelabels with the one just downloaded. Wei Wen Doug Greve wrote: > > This may be a problem with the way that the unix tail command is > implemented in newer OSs. Try copying this file: > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_mergelabe… > > into $FREESURFER_HOME/bin > > doug > > > > Wen, Wei wrote: >> - >> >> Hi >> >> FOrgot to attach the file of lh.cortex.label with my last email. Here >> it is. >> >> >> My error message is the same as Sky's: see >> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07271.html >> >> Looked like there was no solution for it at the time (April 17th, >> 2008), what about now please? >> >> "mri_glmfit: could not parse 149955th line in >> /home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label" >> >> here I have attached the file for you to have a look. Also, I got the >> same error message while trying to load that file using tksurfer. I >> am using your latest version: 4.0.3. >> >> Many thanks and regards, >> >> Wei Wen >> >> ------------------------------------------------------------------------ >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > In order to help us help you, please follow the steps in: > surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > >

2 1

RE: question about qdec analysis
by Teddy Youn 05 May '08

05 May '08

Hi again, I had another question for the listserv about the uses of qdec. After finishing a set of subjects (12 controls and 6 subjects), our group wanted to see if we could use qdec to report the number of voxels that are different (e.g. measuring volume, thickness, etc.) between one group to another. We have searched the tutorial and the faqs and haven't come upon any information on this. Any help you can provide would be great. Thanks in advance, -Teddy Si Youn Doris Duke Clinical Research Fellow '07-'08 North Texas TBI Research Center UT Southwestern Medical Center at Dallas Warren Alpert School of Medicine at Brown University, MD '09 Teddy.Youn(a)utsouthwestern.edu (401)-714-2847

4 3

qdec error: ERROR reading lh.cortex.label
by Wen, Wei 05 May '08

05 May '08

- Hi FOrgot to attach the file of lh.cortex.label with my last email. Here it is. My error message is the same as Sky's: see http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg07271.html Looked like there was no solution for it at the time (April 17th, 2008), what about now please? "mri_glmfit: could not parse 149955th line in /home/wei/working/tmp/ThicknessTest/mas_average/label/lh.cortex.label" here I have attached the file for you to have a look. Also, I got the same error message while trying to load that file using tksurfer. I am using your latest version: 4.0.3. Many thanks and regards, Wei Wen #label , from subject ?? 149955 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_and_S_occipital_inferior.label <== 161841 -35.972 -80.938 -14.778 0.000000 161842 -36.025 -80.450 -14.925 0.000000 161843 -36.168 -79.960 -15.187 0.000000 161844 -36.369 -79.474 -15.497 0.000000 161865 -36.354 -78.002 -13.599 0.000000 161867 -36.528 -77.345 -13.903 0.000000 161868 -36.483 -78.158 -14.174 0.000000 161869 -36.548 -78.357 -14.657 0.000000 161870 -36.642 -78.700 -15.248 0.000000 161871 -36.608 -78.998 -15.795 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_and_S_transverse_frontopolar.label <== 146036 -10.905 63.513 0.864 0.000000 146037 -10.311 63.771 0.461 0.000000 146038 -9.668 64.049 0.119 0.000000 146039 -9.118 63.990 1.468 0.000000 146040 -9.069 63.994 0.641 0.000000 146041 -9.142 64.220 -0.199 0.000000 146042 -8.662 64.313 -0.527 0.000000 146043 -8.242 64.305 -0.873 0.000000 146044 -7.830 64.180 -1.201 0.000000 146045 -7.555 63.686 -0.925 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_cingulate-Isthmus.label <== 160127 -7.666 -50.039 7.988 0.000000 160128 -7.850 -50.539 7.248 0.000000 160129 -7.880 -51.416 7.358 0.000000 160130 -8.133 -51.249 7.034 0.000000 160131 -8.355 -51.022 6.870 0.000000 160132 -9.008 -51.423 6.749 0.000000 160146 -6.602 -51.928 9.675 0.000000 160147 -6.494 -52.915 9.655 0.000000 160148 -6.612 -52.723 9.311 0.000000 160149 -6.776 -52.479 9.052 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_cingulate-Main_part.label <== 159387 -5.951 -52.105 18.145 0.000000 159388 -6.284 -52.819 17.433 0.000000 159389 -6.429 -53.666 16.722 0.000000 159390 -6.370 -55.133 16.645 0.000000 159391 -6.281 -54.872 16.312 0.000000 159392 -6.271 -54.615 15.956 0.000000 159393 -5.798 -55.582 15.234 0.000000 159394 -5.294 -56.347 14.655 0.000000 160144 -6.665 -51.017 11.088 0.000000 160145 -6.548 -51.456 10.332 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_cuneus.label <== 158506 -6.294 -97.747 2.503 0.000000 158524 -2.936 -100.625 3.200 0.000000 158525 -3.227 -100.934 2.843 0.000000 158526 -3.535 -101.211 2.550 0.000000 158527 -3.530 -101.742 3.156 0.000000 158528 -3.623 -101.586 2.690 0.000000 158529 -3.922 -101.332 2.215 0.000000 158530 -4.401 -101.368 2.027 0.000000 158531 -4.958 -101.407 1.950 0.000000 158585 -9.034 -102.177 11.034 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_frontal_inf-Opercular_part.label <== 154781 -52.413 22.664 11.459 0.000000 154782 -52.051 22.183 11.700 0.000000 154783 -51.689 21.756 11.910 0.000000 154784 -51.325 21.366 12.138 0.000000 154785 -50.704 21.338 11.787 0.000000 154786 -50.154 21.292 11.467 0.000000 154787 -49.583 21.259 11.249 0.000000 154788 -49.762 21.956 10.332 0.000000 154789 -49.346 21.604 10.704 0.000000 154790 -48.865 21.134 11.077 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_frontal_inf-Orbital_part.label <== 141383 -46.227 32.825 -12.416 0.000000 141388 -45.129 32.120 -13.124 0.000000 153661 -39.115 25.081 -9.099 0.000000 153662 -38.854 24.865 -9.518 0.000000 153663 -38.597 24.673 -9.991 0.000000 153664 -40.230 24.202 -10.845 0.000000 153665 -39.280 24.334 -10.659 0.000000 153666 -38.241 24.564 -10.452 0.000000 153667 -37.836 24.523 -10.870 0.000000 155046 -35.277 29.256 -3.550 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_frontal_inf-Triangular_part.label <== 154945 -44.113 31.256 1.242 0.000000 154946 -43.499 31.123 1.883 0.000000 154947 -42.707 31.117 2.227 0.000000 154948 -41.944 31.094 2.505 0.000000 154949 -41.224 31.064 2.790 0.000000 154951 -41.059 31.215 2.389 0.000000 154952 -40.487 31.021 3.135 0.000000 154953 -39.739 31.033 3.487 0.000000 154954 -38.975 31.040 3.809 0.000000 154956 -46.567 33.022 -5.832 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_frontal_middle.label <== 152192 -25.422 43.661 36.176 0.000000 152193 -24.903 43.734 36.735 0.000000 152194 -25.629 42.573 36.984 0.000000 152195 -24.961 43.099 37.091 0.000000 152196 -24.314 43.653 37.110 0.000000 152197 -23.587 43.608 37.181 0.000000 152416 -30.374 10.035 55.942 0.000000 152417 -30.087 10.331 55.078 0.000000 154632 -42.273 29.883 22.126 0.000000 154633 -41.890 29.278 22.136 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_frontal_superior.label <== 153256 -9.616 39.556 28.515 0.000000 154301 -5.779 17.835 -13.374 0.000000 154303 -6.088 18.430 -12.378 0.000000 154310 -6.408 24.289 -11.686 0.000000 154311 -6.152 23.606 -11.718 0.000000 154312 -5.731 23.789 -10.621 0.000000 154313 -5.830 23.332 -11.127 0.000000 154314 -5.895 22.878 -11.642 0.000000 154315 -5.730 22.160 -11.492 0.000000 154316 -5.749 21.513 -11.279 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_frontomarginal.label <== 154002 -14.694 59.373 -14.691 0.000000 154003 -15.589 59.375 -14.496 0.000000 154004 -16.414 59.275 -14.199 0.000000 154005 -17.193 59.023 -13.804 0.000000 154006 -16.831 57.484 -13.989 0.000000 154007 -17.411 58.133 -13.734 0.000000 154008 -17.989 58.642 -13.362 0.000000 154009 -18.862 58.195 -12.951 0.000000 154010 -19.776 57.756 -12.603 0.000000 154011 -20.579 57.218 -12.133 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_insular_long.label <== 155461 -37.296 -16.269 11.954 0.000000 155462 -37.344 -17.034 11.741 0.000000 155463 -36.932 -17.759 11.334 0.000000 155464 -36.209 -18.408 10.947 0.000000 155465 -35.496 -18.627 9.625 0.000000 155466 -35.558 -18.810 10.111 0.000000 155467 -35.396 -19.054 10.541 0.000000 160277 -34.093 6.181 -12.864 0.000000 160361 -34.922 4.007 -15.335 0.000000 160364 -34.994 3.723 -16.023 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_insular_short.label <== 160274 -33.550 8.313 -11.801 0.000000 160275 -33.737 7.624 -12.140 0.000000 160276 -33.911 6.939 -12.486 0.000000 160349 -30.434 11.355 -12.792 0.000000 160350 -31.068 10.711 -12.719 0.000000 160351 -31.610 10.009 -12.625 0.000000 160352 -32.132 9.185 -12.492 0.000000 160354 -32.332 8.423 -12.664 0.000000 160355 -32.722 8.315 -12.462 0.000000 160356 -33.242 7.323 -12.647 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_occipital_middle.label <== 161700 -39.141 -88.073 -4.667 0.000000 161701 -38.700 -88.311 -5.199 0.000000 161702 -38.261 -88.651 -5.792 0.000000 161703 -37.928 -89.040 -6.405 0.000000 161705 -38.091 -88.799 -6.756 0.000000 161706 -37.644 -89.489 -7.112 0.000000 161707 -37.363 -89.957 -7.893 0.000000 161708 -37.074 -90.471 -8.686 0.000000 161709 -36.623 -90.988 -9.407 0.000000 161710 -36.697 -90.792 -9.708 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_occipital_superior.label <== 158580 -9.090 -100.791 12.967 0.000000 158581 -9.933 -101.045 13.998 0.000000 158582 -9.441 -101.262 13.235 0.000000 158583 -8.980 -101.330 12.380 0.000000 158587 -12.304 -101.274 13.583 0.000000 158588 -11.736 -101.674 13.045 0.000000 158589 -11.129 -102.092 12.457 0.000000 158590 -11.892 -101.996 11.405 0.000000 158591 -11.216 -102.226 11.676 0.000000 158592 -10.547 -102.345 11.876 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_occipit-temp_lat-Or_fusiform.label <== 163062 -31.296 -40.929 -19.124 0.000000 163063 -30.691 -40.170 -19.804 0.000000 163064 -31.316 -40.303 -19.532 0.000000 163065 -31.985 -40.494 -19.274 0.000000 163069 -31.615 -37.497 -21.873 0.000000 163070 -32.034 -37.515 -21.593 0.000000 163071 -32.311 -37.705 -21.114 0.000000 163072 -33.188 -36.471 -21.657 0.000000 163073 -32.970 -37.124 -21.293 0.000000 163074 -32.852 -37.923 -20.785 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_occipit-temp_med-Lingual_part.label <== 162860 -13.707 -67.162 -4.281 0.000000 162861 -13.194 -66.609 -4.280 0.000000 162862 -13.908 -65.621 -4.484 0.000000 162863 -14.426 -64.728 -4.810 0.000000 162864 -14.949 -63.886 -5.191 0.000000 162866 -15.837 -63.549 -5.293 0.000000 162867 -15.530 -62.971 -5.455 0.000000 162868 -16.127 -62.025 -5.698 0.000000 162869 -16.693 -61.082 -5.931 0.000000 162870 -17.355 -60.080 -6.184 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_occipit-temp_med-Parahippocampal_part.label <== 163815 -29.152 -24.285 -26.093 0.000000 163816 -29.644 -24.235 -25.918 0.000000 163817 -30.317 -24.113 -25.668 0.000000 163818 -31.014 -23.978 -25.404 0.000000 163819 -31.072 -24.627 -24.149 0.000000 163820 -31.155 -24.370 -24.756 0.000000 163821 -31.606 -23.865 -25.128 0.000000 163822 -32.088 -23.739 -24.914 0.000000 163823 -32.573 -23.612 -24.753 0.000000 163824 -33.263 -23.370 -24.428 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_orbital.label <== 160491 -15.787 14.839 -19.651 0.000000 160492 -15.823 14.211 -20.087 0.000000 160493 -15.983 13.627 -20.440 0.000000 160494 -16.567 13.152 -19.985 0.000000 160495 -17.232 12.897 -19.459 0.000000 160496 -17.931 12.658 -18.897 0.000000 160497 -18.178 12.857 -17.546 0.000000 160498 -18.433 12.629 -17.904 0.000000 160499 -18.532 12.474 -18.251 0.000000 160500 -19.198 12.177 -17.662 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_paracentral.label <== 151909 -12.324 -39.858 57.645 0.000000 151958 -14.326 -45.978 63.929 0.000000 152012 -13.246 -43.222 71.272 0.000000 152013 -13.360 -43.948 71.080 0.000000 152014 -13.363 -44.678 70.857 0.000000 152015 -13.274 -45.058 71.360 0.000000 152016 -13.249 -45.164 70.968 0.000000 152017 -13.310 -45.388 70.599 0.000000 152018 -13.162 -46.002 70.328 0.000000 152021 -13.574 -46.866 71.266 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_parietal_inferior-Angular_part.label <== 157658 -31.739 -72.258 40.566 0.000000 157659 -31.308 -72.028 40.581 0.000000 157660 -30.919 -71.806 40.629 0.000000 157661 -30.433 -72.927 40.777 0.000000 157662 -30.475 -72.232 40.707 0.000000 157663 -30.536 -71.635 40.642 0.000000 157664 -30.112 -71.567 40.598 0.000000 157665 -29.621 -71.585 40.458 0.000000 157667 -30.424 -74.680 38.481 0.000000 157668 -30.083 -74.091 38.789 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_parietal_inferior-Supramarginal_part.label <== 156224 -50.932 -41.575 30.020 0.000000 156225 -51.139 -42.024 30.465 0.000000 156226 -50.884 -42.744 30.428 0.000000 156227 -50.709 -43.485 30.283 0.000000 156299 -61.927 -48.839 16.785 0.000000 156300 -62.210 -49.269 16.276 0.000000 156301 -62.107 -48.666 15.766 0.000000 156302 -62.311 -49.144 15.845 0.000000 156303 -62.424 -49.695 15.777 0.000000 156304 -62.501 -50.055 15.246 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_parietal_superior.label <== 157654 -32.037 -74.239 41.725 0.000000 157666 -29.268 -71.552 40.220 0.000000 157669 -29.735 -73.562 39.090 0.000000 157671 -29.680 -73.317 38.501 0.000000 157672 -29.426 -73.066 39.332 0.000000 157673 -29.245 -72.550 39.581 0.000000 157674 -29.089 -72.027 39.757 0.000000 157675 -28.958 -71.477 39.839 0.000000 157676 -28.737 -71.354 39.410 0.000000 157677 -28.571 -71.186 38.977 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_postcentral.label <== 151049 -34.812 -35.969 59.367 0.000000 151050 -34.255 -35.839 59.511 0.000000 151051 -33.835 -35.941 57.907 0.000000 151052 -33.819 -35.777 58.820 0.000000 151053 -33.789 -35.671 59.724 0.000000 151054 -33.178 -35.577 59.872 0.000000 151055 -32.570 -35.453 59.863 0.000000 151056 -31.977 -35.308 59.982 0.000000 151057 -31.485 -35.309 59.084 0.000000 151058 -30.900 -35.369 58.281 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_precentral.label <== 149528 -46.454 -2.022 46.232 0.000000 149529 -47.127 -2.379 46.312 0.000000 149530 -47.036 -2.736 45.739 0.000000 149531 -46.933 -3.035 45.105 0.000000 151715 -12.219 -19.599 74.362 0.000000 151716 -11.821 -19.501 74.455 0.000000 151717 -11.379 -19.343 74.544 0.000000 151718 -11.241 -20.346 75.109 0.000000 151719 -11.087 -19.704 74.930 0.000000 151770 -11.498 -29.188 69.421 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_precuneus.label <== 160151 -7.440 -53.342 8.462 0.000000 160152 -7.947 -53.640 8.473 0.000000 160153 -6.817 -55.811 9.287 0.000000 160154 -7.082 -55.512 9.124 0.000000 160155 -7.402 -55.174 9.062 0.000000 160156 -8.029 -55.824 9.614 0.000000 160157 -7.883 -55.359 9.298 0.000000 160158 -7.650 -54.843 9.016 0.000000 160159 -7.904 -54.519 8.891 0.000000 160160 -8.197 -54.166 8.800 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_rectus.label <== 154278 -3.310 24.714 -21.884 0.000000 154279 -3.346 23.836 -21.714 0.000000 154280 -3.340 22.938 -21.544 0.000000 154281 -3.384 22.049 -21.387 0.000000 154282 -3.674 21.707 -20.842 0.000000 154283 -4.097 21.236 -20.218 0.000000 154284 -4.592 20.675 -19.479 0.000000 154285 -4.966 21.992 -19.132 0.000000 154286 -5.028 21.066 -18.948 0.000000 154287 -5.069 20.165 -18.667 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_subcallosal.label <== 154341 -5.436 14.675 -6.497 0.000000 154342 -5.156 14.283 -5.914 0.000000 154343 -4.908 13.957 -5.389 0.000000 154345 -5.655 17.995 -5.318 0.000000 154346 -5.460 17.221 -5.109 0.000000 154347 -5.260 16.483 -4.917 0.000000 154348 -4.961 16.753 -3.952 0.000000 154349 -5.013 16.255 -4.313 0.000000 154350 -5.046 15.726 -4.738 0.000000 154351 -4.824 14.954 -4.581 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_subcentral.label <== 154371 -57.139 2.135 14.285 0.000000 154372 -57.352 2.095 13.715 0.000000 154373 -57.475 1.988 13.120 0.000000 154374 -57.317 2.528 12.914 0.000000 154375 -57.505 2.242 12.720 0.000000 154376 -57.496 1.851 12.547 0.000000 154377 -57.474 1.680 12.044 0.000000 154378 -57.334 1.405 11.622 0.000000 154379 -57.114 1.184 11.172 0.000000 154380 -57.146 1.418 10.705 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_temporal_inferior.label <== 162233 -49.811 -41.326 -22.085 0.000000 162234 -49.264 -41.706 -22.038 0.000000 162235 -48.952 -40.911 -21.490 0.000000 162236 -48.876 -41.544 -21.816 0.000000 162237 -48.796 -42.227 -22.073 0.000000 162238 -48.335 -42.805 -21.627 0.000000 162250 -49.746 -33.660 -22.384 0.000000 162251 -49.384 -34.446 -21.821 0.000000 162252 -49.197 -35.143 -21.255 0.000000 162255 -48.991 -35.959 -20.743 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_temporal_middle.label <== 161913 -54.636 -56.643 -5.320 0.000000 161914 -54.304 -57.634 -5.375 0.000000 161915 -53.911 -58.454 -5.439 0.000000 161926 -55.968 -48.455 -8.657 0.000000 161927 -55.427 -49.291 -8.621 0.000000 161980 -61.206 -39.319 -15.355 0.000000 161981 -60.807 -40.084 -15.357 0.000000 161982 -60.447 -40.926 -15.488 0.000000 161983 -61.147 -40.871 -16.264 0.000000 161984 -60.766 -41.389 -15.830 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.G_temp_sup-G_temp_transv_and_interm_S.label <== 155301 -54.461 -6.481 -1.419 0.000000 155302 -54.601 -5.728 -1.751 0.000000 155303 -53.520 -6.985 -1.982 0.000000 155304 -54.089 -5.977 -2.017 0.000000 155305 -54.766 -4.884 -2.070 0.000000 155311 -53.557 -3.709 -3.995 0.000000 155312 -53.003 -5.545 -3.696 0.000000 155313 -53.069 -4.836 -4.044 0.000000 155314 -53.097 -4.189 -4.408 0.000000 155315 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0.000000 155052 -31.811 30.348 -1.396 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.Lat_Fissure-ant_sgt-ramus_vertical.label <== 154859 -37.866 21.655 12.133 0.000000 154860 -37.702 22.689 11.913 0.000000 154861 -37.537 22.071 12.191 0.000000 154862 -37.420 21.385 12.450 0.000000 154863 -36.925 21.138 12.722 0.000000 154864 -36.487 20.839 12.967 0.000000 154882 -38.156 25.969 10.774 0.000000 154883 -37.539 25.812 11.175 0.000000 154890 -37.581 26.800 10.570 0.000000 154891 -37.257 26.202 11.070 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.Lat_Fissure-post_sgt.label <== 156254 -48.146 -45.210 21.463 0.000000 156255 -48.702 -45.485 21.345 0.000000 156256 -49.291 -45.225 19.944 0.000000 156257 -49.309 -45.478 20.563 0.000000 156258 -49.272 -45.747 21.257 0.000000 156259 -49.821 -46.001 21.242 0.000000 156260 -50.388 -46.221 21.237 0.000000 156261 -50.980 -46.453 21.233 0.000000 156388 -49.592 -40.053 10.593 0.000000 156389 -50.357 -39.668 10.360 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.Pole_occipital.label <== 158680 -23.581 -100.589 -4.938 0.000000 158681 -23.990 -100.484 -5.569 0.000000 158682 -24.054 -100.238 -6.230 0.000000 158691 -20.099 -98.174 -1.392 0.000000 158692 -20.613 -98.112 -1.906 0.000000 158693 -21.253 -98.144 -2.304 0.000000 162637 -6.495 -94.132 -6.619 0.000000 162638 -6.403 -93.821 -5.683 0.000000 162639 -6.231 -93.634 -5.000 0.000000 162655 -3.624 -97.047 -13.148 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.Pole_temporal.label <== 161500 -42.097 -4.726 -40.528 0.000000 161503 -38.579 -3.287 -42.011 0.000000 161504 -39.340 -3.833 -42.079 0.000000 161511 -43.075 -6.637 -41.261 0.000000 161521 -34.665 -4.173 -41.958 0.000000 161522 -35.072 -4.822 -41.969 0.000000 161523 -35.493 -5.252 -42.118 0.000000 161526 -36.019 -5.659 -41.985 0.000000 161527 -36.696 -6.044 -42.178 0.000000 161528 -37.330 -6.405 -42.017 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_calcarine.label <== 162633 -8.848 -92.920 -1.308 0.000000 162634 -8.597 -92.555 -1.837 0.000000 162635 -8.167 -92.058 -2.369 0.000000 162636 -7.640 -91.621 -2.902 0.000000 162642 -6.321 -93.062 -4.438 0.000000 162643 -6.536 -92.422 -3.967 0.000000 162644 -6.769 -91.773 -3.711 0.000000 162645 -7.036 -91.206 -3.504 0.000000 162646 -6.459 -90.725 -4.201 0.000000 162647 -5.689 -90.479 -4.853 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_central_insula.label <== 155732 -37.576 -2.125 -1.942 0.000000 155733 -37.477 -2.071 -2.377 0.000000 155734 -37.315 -2.017 -2.802 0.000000 155736 -37.558 -0.960 -2.298 0.000000 155737 -37.226 -1.958 -3.207 0.000000 155738 -37.111 -1.906 -3.587 0.000000 155739 -37.126 -1.838 -3.988 0.000000 155740 -37.086 -1.817 -4.440 0.000000 155741 -37.137 -0.900 -3.981 0.000000 155742 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158946 -5.260 -29.363 41.426 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_cingulate-Marginalis_part.label <== 159061 -10.670 -41.226 43.379 0.000000 159062 -10.310 -41.055 43.264 0.000000 159141 -9.006 -42.057 43.650 0.000000 159142 -9.442 -41.463 43.487 0.000000 159143 -9.928 -40.860 43.221 0.000000 159144 -9.444 -40.692 43.158 0.000000 159145 -8.996 -40.577 43.105 0.000000 159146 -8.569 -40.376 43.054 0.000000 159149 -8.237 -40.215 43.048 0.000000 159150 -7.871 -40.080 43.042 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_circular_insula_anterior.label <== 160328 -25.518 15.438 -17.029 0.000000 160329 -25.384 15.580 -16.334 0.000000 160330 -25.300 15.661 -15.751 0.000000 160331 -25.286 15.670 -15.051 0.000000 160332 -25.511 14.996 -14.316 0.000000 160333 -25.977 14.428 -13.768 0.000000 160334 -26.691 13.912 -13.398 0.000000 160335 -26.845 13.285 -13.942 0.000000 160336 -27.154 13.341 -13.526 0.000000 160337 -27.489 13.425 -13.122 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_circular_insula_inferior.label <== 155652 -36.760 -6.394 -7.707 0.000000 155653 -36.751 -5.692 -7.184 0.000000 155654 -36.934 -5.321 -5.753 0.000000 155655 -36.900 -5.150 -6.188 0.000000 155656 -36.906 -5.058 -6.636 0.000000 161170 -49.641 -7.806 -9.921 0.000000 161171 -49.998 -6.496 -9.726 0.000000 161172 -50.302 -5.171 -9.458 0.000000 161173 -50.002 -5.136 -10.458 0.000000 161174 -50.306 -4.454 -9.867 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_circular_insula_superior.label <== 155704 -35.139 2.691 5.374 0.000000 155705 -35.761 1.518 4.840 0.000000 155706 -36.658 0.572 4.393 0.000000 155708 -37.020 0.820 3.631 0.000000 155768 -32.366 14.923 2.650 0.000000 155769 -32.646 15.092 2.342 0.000000 155770 -32.974 15.111 2.057 0.000000 155773 -33.309 15.125 1.770 0.000000 155774 -33.631 15.202 1.492 0.000000 155775 -33.951 15.334 1.238 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_collateral_transverse_ant.label <== 162349 -39.442 -34.084 -21.213 0.000000 162350 -39.068 -34.148 -21.757 0.000000 162352 -39.104 -32.736 -21.567 0.000000 162367 -39.733 -27.808 -20.533 0.000000 162368 -39.589 -28.022 -21.119 0.000000 162369 -39.481 -28.251 -21.455 0.000000 162370 -39.591 -26.141 -21.155 0.000000 162371 -39.336 -27.140 -21.548 0.000000 162372 -39.142 -28.506 -22.176 0.000000 162373 -38.934 -28.567 -22.566 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_collateral_transverse_post.label <== 148980 -29.717 -80.578 -12.488 0.000000 162709 -14.908 -90.166 -8.456 0.000000 162718 -15.541 -86.146 -11.145 0.000000 162736 -19.386 -81.000 -8.461 0.000000 162737 -18.910 -81.411 -8.974 0.000000 162738 -18.363 -81.713 -9.600 0.000000 162739 -18.575 -80.427 -9.828 0.000000 162740 -18.267 -81.208 -10.050 0.000000 162741 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33.430 0.000000 152188 -25.799 41.838 33.840 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_frontal_superior.label <== 152552 -20.123 15.176 54.655 0.000000 152553 -20.449 15.962 54.748 0.000000 152554 -20.237 16.125 55.874 0.000000 152555 -20.449 16.442 55.390 0.000000 152556 -20.781 16.754 54.853 0.000000 152557 -21.090 17.540 54.985 0.000000 152558 -21.481 18.364 55.117 0.000000 152559 -21.749 19.198 55.133 0.000000 152562 -21.038 18.822 57.249 0.000000 152565 -21.197 19.092 56.716 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_frontomarginal.label <== 153966 -17.408 56.744 -8.916 0.000000 153967 -12.679 57.717 -9.180 0.000000 153968 -13.360 57.314 -9.206 0.000000 153969 -14.156 57.055 -9.238 0.000000 153970 -14.063 57.496 -10.821 0.000000 153971 -14.571 57.241 -10.045 0.000000 153972 -15.078 56.987 -9.342 0.000000 153973 -16.052 57.078 -9.425 0.000000 153974 -17.027 57.276 -9.447 0.000000 153975 -18.001 57.607 -9.415 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_intermedius_primus-Jensen.label <== 146996 -52.504 -55.982 23.266 0.000000 146997 -52.820 -56.140 22.810 0.000000 146998 -53.015 -55.362 22.456 0.000000 146999 -53.087 -55.866 22.422 0.000000 147000 -53.143 -56.308 22.396 0.000000 147001 -53.483 -56.592 21.964 0.000000 147004 -54.445 -54.217 20.923 0.000000 147005 -54.486 -54.821 20.968 0.000000 147006 -54.538 -55.431 21.040 0.000000 147009 -54.551 -56.050 21.048 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_intraparietal-and_Parietal_transverse.label <== 157709 -29.400 -71.441 24.779 0.000000 157710 -29.292 -71.816 23.927 0.000000 157711 -29.093 -72.180 23.037 0.000000 157712 -31.207 -78.925 28.211 0.000000 157713 -31.168 -78.451 27.676 0.000000 157714 -31.057 -77.969 27.139 0.000000 157717 -31.025 -77.419 26.569 0.000000 157718 -30.968 -76.944 25.973 0.000000 157719 -30.865 -76.464 25.418 0.000000 157738 -28.863 -72.528 22.150 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_occipital_anterior.label <== 161772 -43.047 -72.859 -6.474 0.000000 161775 -41.364 -72.128 -6.294 0.000000 161779 -42.076 -72.795 -6.426 0.000000 161780 -42.463 -73.185 -6.461 0.000000 161781 -42.886 -73.523 -6.330 0.000000 161845 -36.709 -74.324 -8.122 0.000000 161851 -36.124 -76.214 -10.393 0.000000 161852 -36.054 -76.561 -10.954 0.000000 161853 -35.988 -76.875 -11.462 0.000000 161862 -36.021 -77.193 -11.966 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_occipital_middle_and_Lunatus.label <== 158727 -26.814 -92.401 -4.177 0.000000 158728 -27.108 -92.309 -4.780 0.000000 158729 -27.519 -92.163 -5.230 0.000000 158730 -27.964 -91.916 -5.569 0.000000 158733 -29.877 -90.404 -4.292 0.000000 158734 -29.541 -90.078 -3.662 0.000000 158735 -29.995 -90.094 -3.765 0.000000 158736 -30.512 -90.231 -3.849 0.000000 158737 -31.147 -90.028 -3.376 0.000000 158738 -31.849 -89.926 -2.917 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_occipital_superior_and_transversalis.label <== 157825 -25.189 -92.701 12.119 0.000000 157826 -25.636 -93.206 12.286 0.000000 157827 -26.067 -93.686 12.405 0.000000 157829 -28.352 -91.628 12.040 0.000000 157830 -28.121 -92.142 12.054 0.000000 157831 -27.913 -92.756 12.133 0.000000 157832 -28.808 -93.257 12.305 0.000000 157833 -28.240 -93.300 12.253 0.000000 157834 -27.637 -93.334 12.233 0.000000 157835 -27.325 -93.848 12.357 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_occipito-temporal_lateral.label <== 162274 -45.104 -42.025 -19.587 0.000000 162275 -44.562 -42.489 -19.592 0.000000 162276 -44.056 -42.986 -19.636 0.000000 162277 -43.680 -42.989 -19.874 0.000000 162278 -43.449 -43.004 -20.165 0.000000 162279 -43.161 -43.048 -20.571 0.000000 162280 -43.503 -41.807 -19.928 0.000000 162281 -43.265 -42.517 -20.554 0.000000 162282 -42.892 -43.045 -20.835 0.000000 162290 -42.261 -40.786 -20.515 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_occipito-temporal_medial_and_S_Lingual.label <== 163832 -33.354 -23.546 -23.602 0.000000 163833 -33.715 -23.390 -24.295 0.000000 163834 -34.291 -23.446 -24.165 0.000000 163835 -34.475 -23.361 -23.893 0.000000 163836 -34.938 -23.223 -23.573 0.000000 163837 -35.491 -24.274 -22.150 0.000000 163838 -35.181 -23.946 -22.623 0.000000 163839 -35.535 -23.405 -23.323 0.000000 163840 -35.598 -23.848 -23.352 0.000000 163841 -36.059 -24.136 -22.394 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_orbital-H_shapped.label <== 154054 -18.365 40.006 -15.898 0.000000 154055 -18.941 39.320 -16.219 0.000000 154056 -19.583 38.657 -16.419 0.000000 154057 -18.943 37.946 -16.732 0.000000 154058 -18.172 37.225 -17.142 0.000000 154059 -17.455 36.524 -17.713 0.000000 154060 -16.145 37.467 -18.774 0.000000 154061 -16.480 36.654 -18.604 0.000000 154062 -16.956 35.922 -18.594 0.000000 154063 -16.481 35.415 -19.710 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_orbital_lateral.label <== 141345 -43.915 37.285 -6.954 0.000000 141346 -44.622 36.526 -6.551 0.000000 141347 -45.433 35.996 -6.166 0.000000 146306 -37.709 48.619 3.847 0.000000 146307 -37.429 48.716 3.094 0.000000 146308 -37.414 48.831 2.375 0.000000 146309 -37.320 49.058 1.551 0.000000 146312 -37.253 49.438 0.706 0.000000 146313 -37.407 49.854 -0.151 0.000000 146314 -37.799 50.334 -0.950 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_orbital_medial-Or_olfactory.label <== 160485 -16.460 16.939 -16.413 0.000000 160501 -19.701 11.677 -17.143 0.000000 160502 -20.220 11.174 -16.619 0.000000 160503 -18.424 10.086 -15.269 0.000000 160504 -18.789 10.174 -15.400 0.000000 160505 -19.091 10.337 -15.614 0.000000 160508 -19.513 10.408 -15.614 0.000000 160509 -19.907 10.415 -15.808 0.000000 160510 -20.269 10.464 -16.025 0.000000 160511 -20.585 10.556 -16.258 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_paracentral.label <== 151563 -9.687 -24.803 59.093 0.000000 151564 -9.596 -24.134 58.874 0.000000 151565 -9.312 -25.212 57.751 0.000000 151566 -9.419 -24.329 58.211 0.000000 151567 -9.326 -23.460 58.688 0.000000 151568 -8.800 -22.864 58.500 0.000000 151574 -8.131 -23.706 56.045 0.000000 151583 -7.784 -25.380 53.615 0.000000 151856 -6.659 -33.002 62.415 0.000000 151857 -6.513 -33.658 61.958 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_parieto_occipital.label <== 159451 -14.773 -58.658 14.855 0.000000 159452 -14.819 -58.817 14.309 0.000000 159453 -16.611 -59.290 14.069 0.000000 159454 -15.737 -59.096 13.979 0.000000 159455 -14.850 -58.950 13.799 0.000000 159456 -14.891 -59.042 13.339 0.000000 159457 -14.889 -59.015 12.854 0.000000 159458 -14.936 -58.979 12.430 0.000000 159459 -15.926 -59.283 12.020 0.000000 159462 -18.033 -60.540 11.159 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_pericallosal.label <== 160075 -5.746 -45.890 16.565 0.000000 160076 -5.407 -45.545 17.069 0.000000 160099 -6.062 -46.134 13.289 0.000000 160102 -7.369 -46.646 12.138 0.000000 160110 -8.136 -46.027 10.118 0.000000 160111 -8.773 -46.931 10.571 0.000000 160112 -8.753 -46.695 10.230 0.000000 160113 -8.861 -46.553 9.931 0.000000 160114 -9.515 -47.145 9.694 0.000000 160115 -9.819 -47.694 9.213 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_postcentral.label <== 151394 -40.860 -46.978 41.427 0.000000 151395 -40.829 -47.254 41.316 0.000000 151396 -41.158 -47.529 41.322 0.000000 151399 -42.530 -46.456 41.917 0.000000 151400 -42.433 -46.842 42.017 0.000000 151401 -42.238 -47.147 42.000 0.000000 151402 -42.961 -47.276 42.204 0.000000 151403 -42.521 -47.387 42.105 0.000000 151404 -42.145 -47.540 41.989 0.000000 151405 -42.085 -47.790 41.922 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_precentral-Inferior-part.label <== 154468 -48.926 8.675 13.839 0.000000 154469 -49.205 8.570 13.044 0.000000 154488 -49.034 11.551 16.304 0.000000 154489 -49.068 11.058 15.593 0.000000 154490 -49.091 10.524 14.878 0.000000 154492 -49.362 10.489 14.072 0.000000 154493 -49.117 9.989 14.172 0.000000 154494 -49.149 9.531 13.588 0.000000 154495 -49.278 9.009 12.871 0.000000 154496 -49.478 8.466 12.232 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_precentral-Superior-part.label <== 145541 -17.931 -10.509 61.892 0.000000 145542 -18.225 -10.200 61.481 0.000000 145543 -18.571 -9.980 61.022 0.000000 145544 -18.806 -9.238 60.988 0.000000 145545 -19.090 -8.486 61.001 0.000000 145546 -19.452 -7.698 61.072 0.000000 145547 -19.481 -7.220 61.505 0.000000 145548 -19.561 -6.710 62.003 0.000000 145550 -18.856 -7.260 62.676 0.000000 145565 -16.964 -9.678 64.684 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_subcentral_ant.label <== 138430 -49.907 -10.580 15.269 0.000000 138431 -49.410 -10.503 15.059 0.000000 138433 -48.999 -9.908 13.275 0.000000 138434 -48.707 -10.193 13.891 0.000000 149277 -55.194 1.993 17.025 0.000000 149278 -54.700 2.019 17.370 0.000000 149301 -55.001 2.401 19.357 0.000000 149302 -54.346 2.680 20.276 0.000000 149303 -54.414 2.513 19.710 0.000000 149304 -54.475 2.357 19.143 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_subcentral_post.label <== 146688 -53.847 -18.496 19.380 0.000000 146689 -53.673 -18.689 19.827 0.000000 146690 -53.555 -19.019 20.379 0.000000 146691 -52.600 -19.466 20.729 0.000000 146692 -53.028 -19.395 20.790 0.000000 146693 -53.476 -19.384 20.906 0.000000 146694 -53.406 -19.810 21.431 0.000000 146695 -53.356 -20.330 21.929 0.000000 146696 -53.364 -20.960 22.199 0.000000 146697 -53.015 -21.617 22.437 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_suborbital.label <== 154297 -5.810 19.952 -15.510 0.000000 154298 -5.592 19.250 -15.243 0.000000 154299 -5.450 18.576 -14.967 0.000000 154300 -5.506 18.219 -14.173 0.000000 154302 -6.196 17.499 -12.600 0.000000 154309 -6.713 24.931 -11.653 0.000000 154317 -5.962 20.937 -11.045 0.000000 154325 -6.255 20.801 -10.371 0.000000 154326 -6.146 20.296 -10.829 0.000000 154327 -6.379 19.733 -10.562 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_subparietal.label <== 159358 -8.820 -55.466 22.938 0.000000 159359 -8.695 -54.607 23.255 0.000000 159360 -8.408 -54.405 23.054 0.000000 159361 -8.120 -54.226 22.815 0.000000 159362 -7.799 -54.095 22.573 0.000000 159363 -8.159 -55.679 21.450 0.000000 159364 -7.989 -54.721 21.842 0.000000 159365 -7.548 -53.963 22.310 0.000000 159366 -7.314 -53.828 22.017 0.000000 159367 -7.031 -53.688 21.733 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_temporal_inferior.label <== 161979 -47.197 -62.477 -10.085 0.000000 162059 -47.357 -62.024 -10.361 0.000000 162060 -46.467 -62.290 -9.579 0.000000 162061 -45.826 -62.182 -9.215 0.000000 162062 -45.160 -62.123 -8.944 0.000000 162063 -44.510 -61.903 -8.629 0.000000 162064 -45.772 -60.758 -9.507 0.000000 162065 -44.823 -61.245 -8.873 0.000000 162066 -43.877 -61.747 -8.260 0.000000 162067 -43.192 -61.663 -7.902 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_temporal_superior.label <== 161249 -49.435 -1.719 -24.122 0.000000 161250 -50.069 -2.062 -24.713 0.000000 161325 -48.543 -0.459 -25.755 0.000000 161326 -49.732 -0.394 -27.072 0.000000 161327 -49.250 -0.748 -26.377 0.000000 161328 -48.959 -0.947 -25.635 0.000000 161329 -49.640 -1.456 -25.559 0.000000 161330 -50.374 -1.862 -25.436 0.000000 161331 -51.053 -2.240 -25.242 0.000000 161332 -52.160 -2.284 -25.497 0.000000 ==> /home/wei/working/tmp/ThicknessTest/mas_average/make_cortex_label.tmp.9823/lh.S_temporal_transverse.label <== 155216 -54.314 -17.750 3.959 0.000000 155217 -54.676 -17.801 3.533 0.000000 155218 -55.072 -17.860 3.168 0.000000 155219 -55.770 -17.422 2.810 0.000000 155220 -56.502 -17.051 2.504 0.000000 155221 -57.242 -16.732 2.239 0.000000 155222 -57.094 -16.030 2.381 0.000000 155223 -57.581 -16.235 2.188 0.000000 155224 -58.102 -16.461 2.045 0.000000 155225 -58.938 -16.194 1.979 0.000000

2 1

out of memory issue with selxavg3-sess
by Schadwinkel, Stefan 05 May '08

05 May '08

Hi, I've got a general question about selxavg3-sess. In short, when I try to run the analysis, MATLAB exits with an out of memory issue. My previous studies used a TR of 8 seconds, about 120 Acquisitions per run, 5 runs, and everything worked just fine. I now ran two different pilot studies with a TR of 1 second, 4 runs with 840 Acquisitions each. On this data, sexlavg3-sess causes MATLAB to exit with an out of memory message. My main question is, is this just too much data to process or is there a way to configure MATLAB/change the processing scripts to free more memory or use more swap space to allow processing or could it be an issue with the analysis setup creating way too much data? Here are some more details: I use FS-Fast from the freesurfer 4.0.1. rh9 32bit package. When I run the analysis on my machine (x86_64 linux with 1 GB RAM), I get following error, followed by a Java VM fatal exception: ----------- . . OLS Residual Pass run 1 t= 0.0 Loaded /home/WELTRAUM/STUDY2_TR1_TEST/GMOC/bold/008/gm_run_er.par as a par2 file. ??? Error using ==> unknown Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 413 rsserun = sum(rrun.^2); >> Unable to open file for Java VM logging Opening log file: /home/stefan/java.log.10568 pure virtual method called terminate called without an active exception . -------------------- I assumed, 1 GB might just not enough memory, so I tried the same analysis with just one run and turned off as much as possible of the other options (temporal whitening, motion regressors, etc.). Yet, looking at the analysis.conf resulting from that, I am not sure that turning it off in the mkanalysis-sess -gui had an effect with all options. With that configuration and just one run, the memory problem persisted. Next, I tried it on another linux box with 2GB RAM (same freesurfer version), with similar errors during whitening: ---------------------- . . Whitening Computing whitening matrices ??? Error using ==> zeros Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 501 W = zeros(ntptot,ntptot,flac0.acfbins); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n ------------------------------------- Next, still assuming not enough memory to be the problem, I tried it on a Mac Pro with Mac OS X 10.5 and 4 GB RAM using the current corresponding freesurfer version (freesurfer-Darwin-leopard-i686-stable-pub-v4.0.3-full.dmg). Still, similar memory problems persisted: ----------------- . . Whitening Computing whitening matrices MATLAB(21818,0xb0801000) malloc: *** mmap(size=913952768) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug ??? Out of memory. Type HELP MEMORY for your options. Error in ==> fast_selxavg3 at 505 W = zeros(ntptot,ntptot,flac0.acfbins); >> ------------------------------------------ ERROR: fast_selxavg3() failed\n ------------------------------------ Now, although it could be just too much data to compute, I think I'm not the only person who wishes to analyse data of that size, as it is not really that much. My session consists of 14 Minutes per run with TR=1 and about 8 Blocks per run with an event-related paradigm, resulting in about 16 roughly 32s long blocks to fit with the GLM (per run). Maybe, I simply made some errors in setting up the analysis. Here's one paradigm file of the first run and the analysis.conf: ------------------ 16.000000 0 68.235200 1 99.998800 2 114.000000 0 169.248400 1 201.487000 2 217.000000 0 264.894600 1 300.822200 2 318.000000 0 331.545500 1 356.612700 1 375.654700 2 387.401400 1 410.274400 2 413.000000 0 453.019700 1 508.000000 0 515.996200 2 552.006400 1 603.000000 0 603.923700 2 652.629700 1 699.231800 2 702.000000 0 709.726400 1 753.749600 1 781.971400 2 804.000000 0 ----------------------- ----------- analysis.conf ----------------- cat analysis.cfg -delay 0.000000 -TER 1.000000 -polyfit 2 -gammafit 2.250000 1.250000 -gammaexp 2.000000 -timewindow 24.000000 -prestim 4.000000 -autostimdur ------------------------------------------------ ------------ analysis.info ---------------------- cat analysis.info analysis gmoc_analysis_1 TR 1.000000 fsd bold funcstem fmcstc runlistfile study_runs tpexclude parname gm_run_er.par designtype event-related nconditions 2 Condition 1 Condition01 Condition 2 Condition02 -------------------------------------------------- Thanks in advance, your comments on this issue and the size of the fMRI session is greatly appreciated. Best regards, Stefan Schadwinkel

2 1

thickness file data structure
by Yaroslav Halchenko 03 May '08

03 May '08

Dear Freesurfers, First thanks everyone who helped me out with reading-in .mgh data from within Python (especial thanks to Krish). Now I wonder what actually I got ;-) and please pardon my ignorance When I read in thickness file in I get an array of (23406, 7, 58) dimensionality, where 58 makes sense to me since we have 58 subjects. P.S. I've got the same dimensions whenever I didn't use Krish's python binding but converted to minc and loaded using NetCDF module (in python though again, but python's numpy.ndarray dimensionality is not limited by short) What I wonder about is that why 23406 and 7? ok - the product is equal to the surface number of vertices:23406*7=163842, so it seems that I can simply collapse those two dimensions (which one goes first?) but why is that done so? according to http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MghFormat and mri.h in particular I don't see any limit on width/hight to be of short (not int) type and int (4 bytes) should be good enough to store full index. Is that due to some historical perspective? or am I just completely missing smth? Thanks in advance for the hints! -- Yaroslav Halchenko Research Assistant, Psychology Department, Rutgers-Newark Student Ph.D. @ CS Dept. NJIT Office: (973) 353-5440x263 | FWD: 82823 | Fax: (973) 353-1171 101 Warren Str, Smith Hall, Rm 4-105, Newark NJ 07102 WWW: http://www.linkedin.com/in/yarik

4 4

mris_preproc: multiple volumes from one subject
by Jascha Swisher 02 May '08

02 May '08

Hello all - I"ve come across a slight issue when using mris_preproc to register multiple volumes from one subject onto a common surface. The temporary files created by mri_surf2surf have the name $tmpdir/$subj.mgh, which works just fine when each volume being transformed comes from a different subject. However when transforming multiple volumes from the same subject, each file converted overwrites the previous. The result is that the final call to mri_concat concatenates together multiple copies of the same volume, rather than the separate volumes specified as input. A simple fix is to change the name of the temp files from $tmpdir/$subj.mgh to $tmpdir/$subj.$tinc.mgh, where $tinc is incremented after each volume. I've attached a diff against version 1.37.2.2 of mris_preproc (from Freesurfer 4.0.2) that implements this. cheers... -- jds 82,83d81 < @ tinc = 0; # JDS < 209,210c207 < set tval = $tmpdir/$subj.$tinc.mgh #JDS: added tinc to avoid same-subject collisions < @ tinc = $tinc + 1 # JDS: increment tinc --- > set tval = $tmpdir/$subj.mgh -- Jascha D Swisher Research Associate - Tong Lab Department of Psychology Vanderbilt University 422 Wilson Hall 111 21st Ave S Nashville TN 37203 office: 615.322.2835 cell: 617.584.9881

2 1

about nucleus of thalamus segmentation tool
by abel cruz vadell 02 May '08

02 May '08

Hello I have read in the freeSurferWiki (http://surfer.nmr.mgh.harvard.edu/fswiki/Thalamus#head-f0c8409c96fe3e19d4b7…) about a project to segment the different nucleus of the thalamus. The page have ex-vivo and in-vivo Data Locations but I can´t find them in FreeSurfer. Does FS v 4.02 have these tool? How could I use it? Thanks Abel ______________________________________________ Enviado desde Correo Yahoo! La bandeja de entrada más inteligente.

2 1

vertex correspondence
by Mishkin Derakhshan 01 May '08

01 May '08

Hi, I know that at some point in the pipeline, the surfaces are registered to a common sphere, and thus I'm hopping there is a one-to-one vertex correspondance between subjects. My question is, let's say I look at vertex X, on subject1, how do I find out the corresponding vertex location on subjectN. thanks, mishkin

2 1

Problem with the volume brush
by Matt Colvin 30 Apr '08

30 Apr '08

Dear Free Surfers, Occasionally when using the "edit voxels" tool in Tkmedit, I have experienced a weird problem. The brush radius appears to spontaneously increase, usually to a radius of 2 but sometimes as high as 8 or 10. The results are easy enough to correct by undoing my last edit and changing the brush radius back, but it happens frequently enough that it has become quite annoying. Does anybody have a theory as to what may be causing it? Is it most likely a bug or could I be causing on my own without realizing? Thanks in advance if anybody can help. --Matthew Colvin

1 0

Feedback on Talairach QA and Q about segmentation in several atrophy
by Damian Jenkins 30 Apr '08

30 Apr '08

Using the -notal-check flag after recon-all to bypass Talairach allowed us to reclaim several images for inclusion in a study containing MS patients with severe atrophy. However, one image (which is nearly all ventricle!) is proving difficult to segment. The segmentation process parcels up bits of the ventricular space as thalamus and as caudate. Is there a way around this, or do images with very severe atrophy need to be excluded? Dr Damian Jenkins Department of Clinical Neurology Oxford University

2 1

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